-
REVIEW Open Access
Cyclin-dependent kinases and raredevelopmental disordersPierre
Colas
Abstract
Extensive studies in the past 30 years have established that
cyclin-dependent kinases (CDKs) exert many diverse,important
functions in a number of molecular and cellular processes that are
at play during development. Notsurprisingly, mutations affecting
CDKs or their activating cyclin subunits have been involved in a
variety of rarehuman developmental disorders. These recent findings
are reviewed herein, giving a particular attention to thediscovered
mutations and their demonstrated or hypothesized functional
consequences, which can account forpathological human phenotypes.
The review highlights novel, important CDK or cyclin functions that
were unveiledby their association with human disorders, and it
discusses the shortcomings of mouse models to reveal some ofthese
functions. It explains how human genetics can be used in
combination with proteome-scale interactiondatabases to loom
regulatory networks around CDKs and cyclins. Finally, it advocates
the use of these networks toprofile pathogenic CDK or cyclin
variants, in order to gain knowledge on protein function and on
pathogenicmechanisms.
Keywords: CDKs , Cyclins , Developmental disorders , Regulatory
networks , Interaction profiling
IntroductionCyclin-dependent kinases (CDKs) form a family of
20serine/threonine protein kinases that exert pivotal func-tions in
fundamental cellular and molecular processes,such as cell division,
migration, senescence, death, genetranscription, mRNA splicing,
metabolism, and otherimportant mechanisms (reviewed in [1, 2]. As
indicatedby their name and in addition to post-translational
mod-ifications, they require a physical association with a cyc-lin
partner to become catalytically active and able tophosphorylate
their protein substrates. Over 30 cyclinshave been identified in
humans, on the basis of the pres-ence of a cyclin box domain that
is responsible for bind-ing and activating CDKs. Functional and
phylogeneticstudies distinguish 3 subfamilies of CDK and cyclin
pro-teins (cell cycle, transcriptional, atypical) that form
com-binatorial interactions mostly within each subfamily [3].
Overexpression and/or dysfunction of CDKs or cyclinshave been
reported in a very large number of humancancers and other diverse
pathologies. These protein ki-nases are thus considered as valuable
therapeutic targetsfor drug development. A first set of CDK
selective inhib-itors have been approved recently against
hormone-dependent/HER2-negative breast cancers, and they
holdpromises against other solid tumors [4].The first involvement
of a CDK in a rare disease, fa-
milial melanoma, was reported more than 25 years ago,with the
discovery of pathogenic mutations in theCDKN2 gene that codes for
an inhibitor of CDK4, soonfollowed by the discovery of mutations in
the CDK4gene itself (reviewed in [5]). CDK4 stood splendidly
iso-lated for a long time, with no further CDK or cyclin in-volved
in any other rare disorder. Over the past 12 years,methodological
advances in human genomics and majorefforts invested in the
identification of the genetic causesof human diseases (reviewed in
[6]) have allowed a re-markable series of discoveries linking 6
different CDKs
© The Author(s). 2020 Open Access This article is licensed under
a Creative Commons Attribution 4.0 International License,which
permits use, sharing, adaptation, distribution and reproduction in
any medium or format, as long as you giveappropriate credit to the
original author(s) and the source, provide a link to the Creative
Commons licence, and indicate ifchanges were made. The images or
other third party material in this article are included in the
article's Creative Commonslicence, unless indicated otherwise in a
credit line to the material. If material is not included in the
article's Creative Commonslicence and your intended use is not
permitted by statutory regulation or exceeds the permitted use, you
will need to obtainpermission directly from the copyright holder.
To view a copy of this licence, visit
http://creativecommons.org/licenses/by/4.0/.The Creative Commons
Public Domain Dedication waiver
(http://creativecommons.org/publicdomain/zero/1.0/) applies to
thedata made available in this article, unless otherwise stated in
a credit line to the data.
Correspondence: [email protected] of Integrative
Biology of Marine Models, Station Biologique deRoscoff, Sorbonne
Université / CNRS, Roscoff, France
Colas Orphanet Journal of Rare Diseases (2020) 15:203
https://doi.org/10.1186/s13023-020-01472-y
http://crossmark.crossref.org/dialog/?doi=10.1186/s13023-020-01472-y&domain=pdfhttp://orcid.org/0000-0001-7436-3718http://creativecommons.org/licenses/by/4.0/http://creativecommons.org/publicdomain/zero/1.0/mailto:[email protected]
-
and 4 different cyclins to rare developmental disorders(Table
1). In view of the crucial roles played by CDKsand cyclins in the
regulation of many cellular processesat play during development,
their involvement in a var-iety of human disorders could be
expected. The purposeof this article is to provide a review of
these recent dis-coveries, highlight their surprising contributions
to ourknowledge on CDK / cyclin functions, explain how theycan help
to chart regulatory networks, and plead for theinteraction
profiling of certain types of pathogenic vari-ants to better
understand CDK / cyclin functions and toelucidate disease
mechanisms.
CDK5 and lissencephaly with cerebellar hypoplasiaLissencephalies
are hereditary brain malformations char-acterized by the absence or
paucity of cerebral convolu-tions, causing the brain surface to
appear unusuallysmooth. They form a heterogeneous group of
disorderswith different cortical morphologies and various
associ-ated malformations, caused by mutations on at least 19
genes mostly coding for microtubule structural proteinsor
microtubule-associated proteins (reviewed in [36]).Ten children
coming from a highly consanguineous fam-ily and presenting a rare
form of lissencephaly with cere-bellar hypoplasia (LCH) were
investigated [7]. Inaddition to an extreme form of LCH, they
presented anagenesis of the corpus callosum, microcephaly,
severeneurological defects, thick skin, permanently fixed jointsand
a constellation of facial dysmorphisms. They all diedbetween 2 days
to 3 months after birth from respiratoryfailure. All affected
children presented a homozygouspoint mutation on the splice donor
site in intron 8 ofCDK5, which was not detected in 200
ethnicallymatched control individuals. The involvement of
thismutation in the LCH was further confirmed by a whole-exome
sequencing on one of the patients, in which theonly homozygous
variant that segregated with the dis-ease was CDK5. In contrast
with control fibroblasts,patient-derived fibroblasts contain
undetectable CDK5mRNA and protein expression levels, which
strongly
Table 1 Overview of CDKs and cyclins involved in developmental
disorders
Gene CDK or cyclin subfamily;CDK or cyclin mainpartner(s)
Disease (phenotype MIMnumber)
Inheritance Mutations Functional impact(mechanism)
References
CDK5 Atypical; p25/p35 Lissencephaly 7 with cerebellarhypoplasia
(616342)
Autosomal Recessive Splice site Loss of function (NMD) [7]
CDK6 Cell Cycle; D-typecyclins (CCND1,2,3)
Primary microcephaly 12 (616080) Autosomal Recessive Missense
Loss of function(misslocalization)
[8]
CDK8 Transcriptional;Cyclin C (CCNC)
Intellectual developmentaldisorder with hypotonia andbehavioral
abnormalities (618748)
AutosomalDominant
Missense inkinase domain
Loss of function(dominant negativeeffects?)
[9]
CDK10 Transcriptional;Cyclin M (CCNQ)
Al Kaissi syndrome (617694) Autosomal Recessive - Splice sites-
Deletions- Frameshift
Loss of function (NMD)Misslocalization?
[10, 11]
CDK13 Transcriptional;Cyclin K (CCNK)
Congenital heart defects,dysmorphic facial features,intellectual
developmentaldisorder (617360)
AutosomalDominant
- Missense- Splice site- Nonsense- Frameshift
Loss of function(dominant negative
effects?haploinsufficiency?)
[12–20]
CDK19 Transcriptional;Cyclin C (CCNC)
Bilateral congenital retinal folds,microcephaly and mild
mentalretardation (unavailable)
AutosomalDominant
Chromosomalpericentricinversion
Haploinsufficiency [21]
CCND2 Cell Cycle; CDK6
Megalencephaly-polymicrogyria-polydactyly-hydrocephalussyndrome 3
(615938)
AutosomalDominant
- Missense- Nonsense
Gain of function(stabilization)
[22]
CCNK Transcriptional;CDK12 and CDK13
Intellectual developmentaldisorder with hypertelorismand
distinctive facies (618147)
AutosomalDominant
- Deletion- Missense
Loss of function(haploinsufficiency)
[23]
CCNO Atypical; unknown Primary ciliary dyskinesia 29(615872)
Autosomal Recessive -Frameshift- Missense- Nonsense
Loss of function(truncations, 1 missense)
[24–28]
CCNQ Transcriptional; CDK10 STAR syndrome (300707) X-linked
Dominant - Deletions- Splice site- Frameshift
Loss of function [29–35]
Source: Online Mendelian Inheritance in Man database
(www.omim.org).
Colas Orphanet Journal of Rare Diseases (2020) 15:203 Page 2 of
14
http://www.omim.org
-
suggests nonsense-mediated decay (NMD) of themRNA. Even if a
protein were expressed, the C-terminaltruncation caused by the
mutation would be expected toseverely compromise the structure of
the kinase activa-tion loop, which is required for CDK5 binding to
its ac-tivating proteins p35/25 [37]. In accordance with
thisprediction, this C-terminally truncated form of CDK5fails to
complement a deletion of the PHO85 gene inyeast, whose growth on
galactose is rescued by wild-typeCDK5. It is thus safe to conclude
that this mutationcauses a total loss-of-function of CDK5 [7].CDK5
presents unique features among the CDK fam-
ily. It is activated by p35 and p39, which exhibit no se-quence
similarity with cyclins but adopt a three-dimensional structure
similar to that of a cyclin box.CDK5 is the only CDK that is active
in post-mitotic neu-rons, where it exerts essential functions such
as survival,memory formation, pain signaling. As observed in
anumber of mice knockout studies, it is essential for nor-mal brain
development where it controls neuronal mi-gration, axonal guidance
and synaptic plasticity(reviewed in [38]). Hence, the
loss-of-function of CDK5readily accounts for the dramatic clinical
condition ofthe above-described patients. Interestingly,
heterozygoussilent and intronic mutations in CDK5 have also
beendetected in individuals affected by non-syndromic intel-lectual
disability (NS-ID) [39]. The functional conse-quences have not been
fully explored, but a resultinghypothetic partial
haploinsufficiency might account forNS-ID, in view of the dramatic
effects caused by a totalCDK5 loss-of-function.
CDK6 and primary microcephalyAutosomal recessive primary
microcephaly (MCPH) isa neurodevelopmental disorder characterized
by re-duced head circumference and cerebral cortex size,and
nonprogressive, variable intellectual disability. Sofar, 25 genes
have been associated with MCPH(reviewed in [40]). Ten children
spanning three gener-ations of a consanguineous family presented
MCPHwith sloping forehead and mild intellectual disability.After
exclusion of all known MCPH loci, 49 candidategenes were
scrutinized and a single nucleotide muta-tion was detected in exon
5 of CDK6. It perfectly seg-regated with the MCPH within the
investigated familyand was neither detected in hundreds of control
indi-viduals nor in databases totaling 6500 exomes. Themutation
substitutes alanine 197 for a threonine,which abrogates the
localization of CDK6 on centro-somes during mitosis, disorganizes
the mitotic spin-dles and affects nuclear morphology.
Patient-derivedfibroblasts present a lower growth rate and a
higherrate of apoptosis than control cells [8]. It is worthnoting
that other genes involved in MCPH play
important roles in mitotic spindle orientation and incentrosome
assembly and separation, which under-scores the importance of this
organelle in neurodeve-lopment [40].CDK6 is a key player in the
control of the transition
from the G1 to the S phase of the cell cycle. Akin toCDK4, it
associates with D-type cyclins and phosphory-lates members of the
retinoblastoma (Rb) tumor sup-pressor family. This results in the
release of E2Ftranscription factors that control the expression of
genesinvolved in cell cycle progression and DNA
replication(reviewed in [41]). The effects produced by the
MCPH-causing mutation are presently unknown. Thesubstituted residue
is located in a loop that is distantfrom the catalytic center and
from the cyclin or the INKinhibitor binding interfaces. Since
patient fibroblasts andCDK6-knockdown cells present similar
defects, the mis-localization of CDK6 is suspected to cause a loss
offunction that is not compensated by its close paralogCDK4 [8].
Interestingly, this pathogenic mutation mightonly cause a loss of
the centrosome-associated functionsof CDK6, while preserving its
transcriptional functionsthat are particularly important in
hematopoiesis [41]. Insupport of this hypothesis, no immunity
defect has beenreported in these MCPH patients [8].
Cyclin D2 and
megalencephaly-polymicrogyria-polydactyly-hydrocephalus
syndromeMegalencephaly-polymicrogyria-polydactyly-hydroceph-aly
(MPPH) syndromes are brain and head overgrowthdisorders associated
with distal limb malformations, in-ducing delayed development and
intellectual disability.Germline mutations in the CCND2 gene coding
for cyc-lin D2 were detected by whole-exome sequencing inthree MPPH
patients who did not present mutations ingenes previously involved
in the syndrome. De novo het-erozygous CCND2 mutations were then
detected in 9additional MPPH cases. Nine of the 12 cases
presentmissense mutations on threonine 280 or proline 281, 2cases
present a mutation that produces a stop codonafter amino acid 270,
and 1 case contains a missensemutation affecting valine 284. All 3
substituted residuesare highly conserved, and the truncated 270
amino acidprotein is likely to be expressed since the mutation
oc-curs in the final exon [22]. More recently, two
additionalindividuals were described, presenting a missense
muta-tion on threonine 280 and proline 281, and an expandedcerebral
and cardiac phenotype, respectively [42, 43].Cyclin D2 was already
known to be phosphorylated on
threonine 280 by GSK-3β and p38MAPK, which triggersits
degradation by the proteasome as demonstrated bythe resistance of a
T280A cyclin D2 mutant toubiquitin-dependent degradation [44]. All
mutatedforms listed above were found to be stabilized and to
Colas Orphanet Journal of Rare Diseases (2020) 15:203 Page 3 of
14
-
accumulate when expressed in a human cell line, in con-trast to
wild-type cyclin D2 [22]. Hence, mutations inCCND2 causing MPPH
induce a gain-of-function of cyc-lin D2. The importance of cyclin
D2 T280 and P281 res-idues for the development of ventricular
andsubventricular zones (VZ and SVZ) in mouse embryoswas examined
by electroporating CCND2 expressionconstructs in utero. These
elegant experiments showed astrong association between the
expression of CCND2mutants found in MPPH and actively dividing
cells, con-trary to the expression of wild-type CCND2. This
indi-cates that stabilized cyclin D2 supports
abnormalproliferation, which yields an increased population
ofneural progenitors (radial glial cells and intermediateprogenitor
cells) that could account for the megalence-phaly observed in MPPH
[22].The opposite phenotypes produced by CDK6 loss-of-
function and cyclin D2 gain-of-function mutations(microcephaly
vs megalencephaly, respectively) are re-markably predictable
considering that the two proteinsheterodimerize to produce an
active protein kinase. Itsuggests that CDK6 and cyclin D2 are
faithful partnersin the control of neural progenitor cell division,
which isnot always observed with other CDK/cyclin pairs
con-trolling other mechanisms. In direct support of this
hy-pothesis, cyclins D1 and D2 show both overlapping anddistinct
expression patterns during mouse forebrain de-velopment, which
indicates that both cyclins exertunique functions in neurogenesis
[45].
Cyclin M and STAR syndromeA novel developmental disorder was
identified in four un-related girls and in a previously reported
mother-daughterpair [29, 46]. Because the cardinal features of the
syn-drome include toe syndactily, telecanthus and anogenitaland
renal malformations, the disorder was dubbed “STARsyndrome”. All
individuals suffer from growth retardation,and additional anomalies
affecting heart, eyes and/or cra-nial bones are observed in some of
them. All six casespresent heterozygous deletions or point
mutations affect-ing the FAM58A gene, located on the
X-chromosome.Over the past decade, very few other STAR syndrome
pa-tients have been reported, some of them presenting add-itional
features such as hearing loss, multiple oculardefects, tethered
spinal cord, skeletal anomalies, or laxjoints [30–34]. The only
lethal form reported so far in-cluded yet additional anomalies such
as cleft lip palate, ab-dominal wall defect and cerebral
malformations [35].Since most of these additional features,
including thoseseen in the lethal case, are associated to large
deletionsthat extend beyond the FAM58A locus, the loss of
neigh-boring genes is suspected to contribute to these
expandedphenotypes [29, 31, 35]. All mutations or deletions
appearto be sporadic except for the four mother-daughter pairs
identified so far [29, 32–34]. In one of these pairs, mater-nal
mosaicism with a minor toe syndactily phenotype wasdetected, which
indicates that gonadal mosaicism is pos-sible [34]. Total or
close-to-total X-inactivation skewingwas observed whenever it was
investigated, thus suggest-ing that cells carrying the mutation on
the active Xchromosome present a growth disadvantage during
devel-opment. This finding is congruent with the fact that
STARsyndrome has never been found to affect males.The functions of
the FAM58A gene were totally un-
known when STAR syndrome was first described. A fewyears later,
the FAM58A gene product was shown to bethe activating cyclin (then
named cyclin M) of CDK10,which was standing out as one of the last
orphan cyclin-dependent kinases, with no identified regulatory
subunit.The CDK10/CycM heterodimer is an active protein kin-ase
that phosphorylates the ETS2 oncoprotein, a previ-ously identified
binding partner of CDK10. Importantly,the truncated cyclin M
proteins that might be expressedfrom two STAR FAM58A mutated forms
are unable tobind CDK10 [47]. Since the majority of the other
allelicvariants consist of large deletions or splice site
muta-tions likely to prevent cyclin M expression, it can
beconcluded that the CDK10/CycM protein kinase is defi-cient in
STAR syndrome. The phosphorylation of ETS2by CDK10/CycM positively
controls ETS2 degradationby the proteasome. As expected, STAR
patient-derivedcells present higher ETS2 protein levels than
controlcells [47]. Interestingly, some morphologic features ofSTAR
syndrome patients might be caused by abnormallyhigh ETS2 levels,
which, in Ets2 transgenic mice, cause anumber of cranial and
skeletal defects [48]. It was latershown that the silencing of
cyclin M, or that of CDK10,promotes assembly and elongation of
primary cilia.These experimental findings combined with the
observa-tion of abnormal, elongated cilia on a STAR patientrenal
biopsy, strongly suggest that STAR syndrome isyet another
ciliopathy [49].
CDK10 and Al Kaissi syndromeNine individuals from five families
presenting growth re-tardation, spine malformation, facial
dysmorphisms, de-velopmental delay and intellectual disability
wereinvestigated and shown to harbor homozygous muta-tions in the
CDK10 gene [10]. All mutations result inframeshifts or internal
truncations that reduce CDK10levels probably through NMD of the
mRNAs. This med-ical condition can thus be attributed to a
loss-of-function of CDK10. Accordingly, enhanced ETS2 proteinlevels
are detected in patient fibroblasts and a mouseCDK10 knockout model
partly replicates the phenotypeobserved in the patients,
particularly skeletal defects[10]. Here again, as could be
expected, these skeletal de-fects are reminiscent of those of ETS2
transgenic mice
Colas Orphanet Journal of Rare Diseases (2020) 15:203 Page 4 of
14
-
[48]. Simultaneously, another study reported one patientwith
globally similar defects and additional features, at-tributed to a
homozygous single nucleotide deletion inthe 11th of the 13 exons of
CDK10 [11]. In contrast tothe above-described cases, the mRNA does
not undergoNMD and it even appears to be slightly upregulated.
Un-expectedly, patient fibroblasts present shorter, less abun-dant
primary cilia [11], whereas RNAi-mediated CDK10silencing in a human
cell line or CDK10 knockoutmouse embryonic fibroblasts exhibit
longer, more abun-dant cilia [10, 49]. This reported mutation
results in aframeshift that might allow the translation of a
shorterCDK10 protein (307 amino acids vs 360 for the
longestwild-type isoform), containing 17 missense amino acidsat its
C-terminus. If expressed, this truncated CDK10would be devoid of
the C-terminal bipartite nuclearlocalization sequence present in
the wild-type protein[50]. It thus might keep some of its
extranuclear func-tions, among which is the regulation of actin
dynamicsand ciliogenesis [49]. It is also worth noting that
thismutated, recessive allele is found in 36 of the 141,000healthy
individuals whose genomes have been depositedon the gnomAD database
[51]. Almost all carriers are ofAshkenazi-Jewish descent, which
represents a remark-ably high carrier rate of 1/290 in this
community.The significant differences between the STAR and the
Al Kaissi syndromes suggest that CDK10 and/or cyclinM exert more
functions than those exerted by theCDK10/CycM protein kinase.
However, as previouslyobserved with other CDKs and cyclins, it is
also possiblethat other members of these two protein families
(suchas cyclin G2 [52]) partially compensate the loss ofCDK10 or
cyclin M to fulfill at least some of the func-tions of the
CDK10/CycM protein kinase.
CDK13 and a congenital heart defect, craniofacial
andintellectual development syndromeCDK13 was associated to a
developmental disorder bytwo recent exome-wide studies on large
patient popula-tions. First, the exomes of < 1900 patients
suffering fromsyndromic and nonsyndromic congenital heart
defectswere sequenced and analyzed, in order to identify
andcharacterize damaging de novo mutations (DNMs). 12genes with
genome-wide significance were shown topresent an excess of DNMs,
among which was CDK13[12]. Second, pursuing the same objective, the
exomes of4300 families containing individuals suffering from
de-velopmental disorders, and those of another 3300 indi-viduals
with similar problems were analyzed. Ninety-four genes were found
significantly enriched in DNMs,among which was CDK13 again, the
only CDK / cyclinfamily member identified in this study [13]. To
date, atotal of 52 patients carrying heterozygous mutations inCDK13
have been reported [12, 14–20]. Their cardinal
features include developmental delay, craniofacial de-fects,
intellectual disability, feeding problems and, in halfof the cases,
structural brain and heart anomalies. Athorough clinical
delineation of the syndrome has beenreviewed recently [18, 53]. In
the last reported case [19],the patient presented with
pseudohypoaldosteronism, adisorder characterized by salt wasting
resulting from tar-get organ unresponsiveness to
mineralocorticoids. It re-mains to be determined whether this
additional featureis coincidental or attributable to the mutation
in CDK13.With more than 1500 amino acids, CDK13 is an un-
usually large CDK that contains an expanded serine-arginine
(SR)-rich region in its N-terminal part, inaddition to the central
protein kinase domain. As ex-pected from a SR domain-containing
protein, CDK13 isinvolved in pre-mRNA splicing regulation and
interactswith other splicing factors [54]. Its regulatory subunit
iscyclin K [55]. The CDK13/CycK protein kinase, akin toother
so-called transcriptional CDKs, phosphorylates theC-terminal domain
(CTD) of RNA polymerase II andcontributes to the control of gene
expression [56]. Thevast majority of the clinical cases reported so
far (41/52)present missense mutations affecting the kinase
domain,more than half of which targeting the highly
conservedasparagine 842. One case presents a missense
mutationupstream of the kinase domain, three cases presentsplice
site mutations in the kinase domain, two casespresent nonsense
mutations in the C-terminal extensionof the kinase domain, and five
cases present a frameshiftor a nonsense mutation that truncate the
protein up-stream of the kinase domain (reviewed in [53]).
Thefunctional consequences of these mutations remain un-certain.
Simple haploinsufficiency resulting from an im-paired kinase
activity seems unlikely, since a number ofloss-of-function
mutations have been identified in thegnomAD database that excludes
genomes of individualssuffering from severe pediatric diseases.
Based on thecrystallographic structure of the CDK13/CycK
complex[56], the modeling of a number of missense variants andof
one of the two splice mutants predicts a preservedability to
interact with cyclin K and a likely loss of cata-lytic activity
[16]. Such variants would act as dominantnegative mutants by
sequestering cyclin K from theCDK13 wild-type allele, a
well-described inhibitorymechanism for CDKs [57]. However, CDK13
haploinsuf-ficiency might contribute to the disease in the 5
casesthat present truncating mutations upstream of the kinasedomain
[18, 20].
Cyclin K and a neurodevelopmental disorder/facialdysmorphism
syndromeRecently, a new syndromic neurodevelopmental disorderwith
facial dysmorphism was described in four unrelatedindividuals, who
harbor de novo heterozygous changes
Colas Orphanet Journal of Rare Diseases (2020) 15:203 Page 5 of
14
-
affecting CCNK (cyclin K coding gene) [23]. Three pa-tients
present specific deletions in the 14q32.3 region,which overlap on
three genes in addition to CCNK. Stat-istical considerations
designated CCNK as the prime sus-pect, and its involvement was
further established by thefinding of a missense mutation (K111E) in
a fourth indi-vidual with similar phenotypic presentations. These
in-clude impaired intellectual, motor, language skills and
aconstellation of facial dysmorphisms. The mutated resi-due being
located at the interaction interfaces withCDK13 [56] and CDK12
[58], the amino acid substitu-tion is expected to destabilize both
complexes and henceto inhibit both kinases [23]. Haploinsufficiency
is thusthe most likely pathogenic mechanism in all
fourpatients.Little is known on the roles of CDK13 and cyclin K
in
development. In mouse, cyclin K-dependent protein ki-nases
maintain self-renewal of embryonic stem cells [59]and CDK13 (and
12) positively regulate axonal elong-ation by controlling CDK5
expression [60]. CNNKknockdown and knockout experiments in
zebrafish pro-duce some dismorphic features that are reminiscent
ofthose observed in the four patients, thereby confirming arole of
cyclin K in neurodevelopment [23]. As for thesyndromes caused by
mutations affecting cyclin M andCDK10, the only partial phenotypic
overlap between thesyndromes caused by CDK13 and CCNK mutations
canbe explained by the fact that at least two different pro-tein
kinases (CDK13 and CDK12) are affected by CCNKhaploinsufficiency.
However, the suspected capacity ofmany CDK13 pathogenic mutants to
sequester cyclin Kin inactive complexes would predict a dominant
negativeeffect on both CDK13 and CDK12 kinases. Another
ex-planation could be that cyclin K exerts functions inde-pendently
from CDK12 or CDK13, and mingles withother CDKs such as CDK9
[61].
Cyclin O and congenital mucociliary clearance disorderMultiple
motile cilia (MMC) are present on a number ofepithelia (such as
those found in lungs) and their beatplays a crucial role in
clearing airways from debris, parti-cles and microbes. Reduced
ciliary motility results inmucociliary clearance disorders such as
cystic fibrosisand primary ciliary dyskinesia (PCD) (reviewed in
[62]).A new type of mucociliary clearance disorder was re-ported in
16 individuals from different consanguineousfamilies, suffering
from recurrent respiratory symptoms(upper and lower airway
infections, evolutive damagesand thickening of bronchial tubes).
Whole-exome se-quencing revealed seven different homozygous
muta-tions occurring in the 3 exons of the CCNO gene thatcodes for
cyclin O. Fifteen of the 16 patients presentmutations that predict
truncated forms the protein (88to 321 amino acids out of 350 for
the wild-type), if they
are expressed. One patient presents a missense mutationaffecting
the highly conserved histine 239 residue [24].Additional cases and
mutations were reported subse-quently, including a missense
mutation affecting leucine213, another highly conserved residue
[25–28]. Respira-tory epithelial patient cells show complete
absence or se-vere reduction of cilia numbers and a marked
decreaseof basal bodies, attributed to an improper amplificationand
migration of the centrioles that nucleate ciliary axo-nemes [24,
26]. None of the putative truncated forms ofcyclin O could be
detected in patient cells (including a321 amino acid-long
theoretical variant) [24]. Moreover,contrary to wild-type cyclin O,
the pathogenic L213Pmutated form does not increase the number of
basalbodies when expressed in Xenopus skin cells [26]. Allmutations
are thus considered loss-of-function. Cyclin Oexpression is
detected in the apical cytoplasm of respira-tory epithelial cells,
which supports a role in mothercentriole amplification [24]. It is
also detected in murineepithelial cells of other multiciliated
tissues such asependymal cells in the developing brain and the
fallopiantubes of juvenile and adult mice, with no
apicallocalization in the latter [26]. This strongly suggests
thatcyclin O participates in the generation of MMCs
duringdevelopment, possibly in association with a still
uniden-tified CDK.
CDK19 / CDK8 and syndromic developmental disorderswith
intellectual disabilityA single female patient was investigated for
presentingwith bilateral congenital retinal folds, microcephaly,
scat-tered café-au-lait skin pigmentations, moderate psycho-motor
retardation and hearing loss. Karyotypingrevealed a de novo
heterozygous pericentric inversion inchromosome 6, and comparative
genomic hybridizationruled out large copy number anomalies. The
breakpointswere precisely mapped and one of them was found toaffect
intron 1 of CDK19, whose transcript level inpatient-derived cells
was found to be half of that of con-trol cells. Since no anomaly
was detected in the secondcopy of the gene, the patient’s condition
is most likelycaused by a CDK19 haploinsufficiency [21].More
recently, 8 heterozygous missense mutations in
CDK8 were found by whole-genome or whole-exome se-quencing in 1
and 11 patients enrolled in a craniosynos-tosis and a developmental
disorder cohort, respectively.Their phenotypic presentations are
variable and com-plex. Mild to moderate developmental delay is a
univer-sally shared feature. Facial dysmorphisms, hypotoniacausing
motor delays, and behavioral symptoms such asautism spectrum
disorder and/or attention deficit hyper-activity are very
frequently observed. Other diverse de-fects are observed less
frequently: agenesis or thinning ofcorpus callosum, sensorineural
hearing loss,
Colas Orphanet Journal of Rare Diseases (2020) 15:203 Page 6 of
14
-
ophtalmological and/or ano-rectal abnormalities, con-genital
heart defects. Only one patient presents cranio-synostosis [9].
Seven mutations were detected only once,whereas the S62L variant
was present in 5 patients.None of these mutations were found in the
commonvariation databases and they arose de novo in the 10cases
whose paternity could be confirmed and analyzed[9].The molecular
and structural consequences of the 8
detected mutations were carefully examined and dis-cussed [9].
They all cluster within the kinase domain,around the ATP binding
pocket. None of them causemajor protein instability and all mutants
retain the abil-ity to bind ATP and cyclin C. However, they all
show apartially reduced kinase activity on the STAT1 substratewhen
expressed in a CDK8−/−/CDK19−/− cell line. Al-though all these
observations would point haploinsuffi-ciency as being the
pathogenic mechanism, the absenceof truncation-inducing mutations
or deletions is quitesurprising, since these defects usually
account for morethan half of the haploinsufficiencies detected in
develop-mental disorders [13]. Moreover, CDK8 is
moderatelyconstrained to loss of function and it presents 6
bonafide truncating alleles listed in the gnomAD
database,suggesting that heterozygous, truncated
loss-of-functionCDK8 variants occur at low frequency in healthy
individ-uals. These considerations strongly argue against
hap-loinsufficiency and rather support a dominant-negativeactivity,
assuming that an only partial loss of CDK8 ac-tivity can produce
important effects during development.The heterogeneity of the
phenotypic presentations can-not be easily linked to the different
missense mutations,and it might stem from minor variations in the
residuallevels of CDK8 activity.CDK8 and CDK19 are highly similar
CDKs (> 90% se-
quence homology) that both interact with cyclin C toform two
distinct mediator kinase modules. Mediator ofRNA polymerase II is
an evolutionary conserved multi-subunit protein complex that
bridges transcription fac-tors to the basal transcriptional
machinery (Pol II andthe TFII general transcription factors),
thereby control-ling the assembly of the preinitiation complex on
genepromoters. The up to 30 protein components of Medi-ator form 4
distinct modules, among which is the CDKkinase module, containing
either CDK8/CycC orCDK19/CycC, associated to MED12 and MED13
orMED12L and MED13L, respectively. Phosphorylation ofMediator
subunits, transcription factors and componentsof the basal
transcriptional machinery plays a pivotalrole in transcriptional
regulation, and CDK8/CDK19take their part together with other CDKs
and other ki-nases (reviewed in [63]). CDK8 is known to regulate
anumber of signaling pathways that play important rolesduring
development (such as Notch, Wnt/β-catenin,
Sonic Hedgehog) (reviewed in [64]), which can explainthe
constellation of defects produced by CDK8 muta-tions. CDK19
transcripts are highly expressed in fetaleye and fetal brain human
tissues [21]. However, the roleof the CDK19 kinase module during
development re-mains poorly understood and is worth exploring in
lightof the human phenotype caused by a haploinsufficiency.
Human developmental syndromes reveal CDK/cyclinfunctionsFor a
number of CDKs and cyclins involved in the devel-opmental disorders
reviewed above, the pathologicalphenotypes could be more or less
accurately predictedfrom the biological knowledge that has
accumulated forup to 25 years, sometimes with the help of mice
knock-out models. An excellent example is provided by CDK5,whose
pivotal role in the development of the central ner-vous system has
been well documented [38]. CDK5 miceknockouts present an abnormal
corticogenesis with lackof neuronal lamination and a cerebellar
hypoplasia, asobserved in CDK5 mutated patients (reviewed in
[36]).Another example is cyclin D2, whose role in
neuronaldevelopment has been identified [2] and whose mouseknockout
models show a loss of cortical intermediateprogenitor cells,
laminar thinning and microcephaly[65], in congruence with the
megalencephaly caused bygain-of-function mutations in
humans.However, in most cases reviewed herein, human phe-
notypes have provided novel, important information onthe
functions of CDK or cyclin genes targeted by patho-genic mutations.
The fact that STAR syndrome presentsfeatures that are frequently
observed in ciliopathies, suchas renal, retinal and digital
anomalies, prompted the ex-ploration of a putative role of
CDK10/CycM in ciliogen-esis. This led to the demonstration that
this proteinkinase promotes assembly and elongation of primarycilia
through the disruption of the actin network involv-ing a PKN2-RhoA
regulatory axis [49]. Without STARsyndrome, the role of CDK10/CycM
in ciliogenesiswould probably be still unknown, especially if one
con-siders that CDK10 was not retained among the hits of
asub-genome-scale RNAi screening that identified a num-ber of novel
modulators of ciliogenesis and cilium length[66]. Another
remarkable illustration of the contributionof human genetics to
fundamental knowledge concernscyclin O, whose functions were almost
totally obscureuntil its involvement in a mucociliary clearance
disorderwas unveiled [24]. Studying this syndrome allowed
todiscover that cyclin O drives the formation of MMCsduring
development by controlling the proper formationof deuterostomes and
the amplification of centrioles.This role was subsequently
confirmed by CCNO knock-down in Xenopus [24] and knockout in mice
[67], wherecyclin O deficiency was shown to compromise
Colas Orphanet Journal of Rare Diseases (2020) 15:203 Page 7 of
14
-
deuterosome-mediated generation of MMCs in multici-liated cells.
Another kind of case study is CDK6, which,akin to all cell cycle
CDKs, has been quite extensivelystudied for more than two decades
and is even one ofthe targets of the first clinically approved CDK
inhibitors[4]. Yet, it is the finding that CDK6 mutations cause
aMCPH syndrome that led to the discovery of thelocalization of CDK6
in centrosomes of dividing cells.The suggested novel role in
centrosome function wasconfirmed by RNAi-mediated knockdown
experiments,and patient-derived and CDK6 knowkdown cells werethen
shown to present reduced motility and polarity [8].
CDK/cyclin human disorders are variably phenocopied bymouse
modelsIn line with the tremendous interest that CDKs andcyclins
have attracted, animal models and in particularmouse knockouts have
been produced for most mem-bers of both families. As presented
above, such modelshave proven very useful in deciphering the
functions ofsome CDKs and cyclins, and they have sometimes of-fered
valuable phenocopies of human syndromes causedby loss-of-function
mutations. However, in other cases,animal models have partially or
totally failed to do so.For example, Cdk10 KO mice phenocopy the
growth re-tardation and the spine defects observed in CDK10-mutated
patients, but they present many additional de-fects in lung,
kidney, heart, spleen, liver, muscle that arenot seen in patients
and that cause massive lethality be-fore or soon after birth [10].
Whereas CCNK haploinsuf-ficiency causes a number of human
anatomical andfunctional phenotypes that should be potentially
detect-able in mice, Ccnk+/− pups and adults are perfectlyhealthy
and reproduce well [55]. Whereas respiratoryproblems represent the
cardinal feature of patients con-taining homozygous
loss-of-function CCNO mutations,none of those conditional KO
Ccno−/− mice that survivedgestation presented such problems.
However, Ccno condi-tional and constitutive KO mice present
hydrocephalusand/or infertility [67, 68], two features occasionally
ob-served in cyclin O-deficient patients [26, 69].
Whereasheterozygote Cdk8+/− mice show no phenotype, it is
im-possible to obtain Cdk8−/− offspring or even late embryos[70].
CDK19 KO mice seem to show no significant func-tional or behavioral
phenotype except for increased gripstrength in males
(www.mousephenotype.org).Many reasons can explain the frequent
inability of
mouse KO models to phenocopy human disorderscaused by mutations
on a number of CDK or cyclingenes. First, it is well known that
functional redundan-cies exist amongst the CDK and, even more so,
the cyc-lin family. Hence, single gene KOs often produce no
ormodest phenotypes due to compensatory mechanisms(reviewed in
[71]). Such redundancies and compensatory
mechanisms also exist in humans. However, despite tre-mendous
progresses [72], mouse phenotyping does notequal human full
clinical investigations, and many hu-man phenotypes (especially
intellectual or behavioralabilities) can hardly be detected in
mice. Second, mouseKO models only have the potential to phenocopy
humansyndromes caused by loss-of-function mutations. Anumber of
syndromes reviewed herein are caused bygain-of-function or
dominant-negative mutations, which,in the latter case, can
conceivably preserve some of thefunctions of the corresponding
protein. With the recentadvances in genome editing techniques, it
is now pos-sible to introduce those mutations in mice to model
hu-man pathological conditions caused by gain-of functionor
dominant-negative mutations [73].
Human genetics looms CDK/cyclin regulatory networksMutations on
different loci often produce overlappinghuman phenotypes or, in
some cases, a single given syn-drome. This frequently reflects
physical and/or func-tional interactions formed between the
correspondingproteins to control underlying biological
mechanisms.An emblematic example is the Bardet-Biedl ciliopathythat
can be caused by mutations on more than 20 so-called BBS genes.
Eight of these genes code for proteinsforming an octameric complex
(the BBsome), whichplays a pivotal role in ciliogenesis [74].
Another one isprovided by a number of syndromes that all include
neu-rodevelopmental disorders and that are caused by muta-tions on
components of the mediator of RNApolymerase II. In particular, 5 of
the 7 proteins that formthe kinase module, among which CDK8 and
CDK19, areinvolved in these mediatorpathies [9, 75]. As
highlightedby the few chosen examples below, the involvement ofCDK
and cyclin genes in human syndromes can point tounknown protein
interactions or can give weigh to puta-tive protein interactions
identified by high-throughputproteome-scale endeavors, within a
number of regula-tory networks.Most of the 20 genes involved in
lissencephaly are re-
lated to microtubule structural or associated-proteins[36]. CDK5
was an already well-known regulator ofneuronal cytoskeleton
dynamics, directly or indirectlyengaging some of these 20 proteins
(reviewed in [76]).The recent discovery of a new lissencephalic
syndromecaused by mutations in CEP85L allowed to unveil an
im-portant interaction with CDK5, which drives thelocalization and
activation of the kinase at the centro-some to ensure proper
organization of centrosome andcytoskeleton [77] (Fig. 1).Autosomal
recessive primary microcephaly can be
caused by mutations on 25 different so-called MCPHgenes and a
large proportion of them, including CDK6,regulate centrosomes and
mitotic spindle [40]. A
Colas Orphanet Journal of Rare Diseases (2020) 15:203 Page 8 of
14
http://www.mousephenotype.org
-
systematic effort to identify CDK4/6 phosphorylationsubstrates
revealed that MCPH10 (aka ZNF335) is phos-phorylated by CDK6/CycD
in vitro [78]. BCL11A, an-other identified zinc finger
phosphorylation substrate, isinvolved in the Dias-Logan syndrome
that includesmicrocephaly among other features [79]. Interestingly,
inmice, Bcl11a deficiency was shown to downregulateCdk6 [80], which
strengthens the hypothesis of a func-tional interplay between both
proteins. Other CDK6/CycD in vitro phosphorylation substrates
include SNIP1,SOX10, TRAK1 and SOX5, which are all involved in
dif-ferent human neurodevelopmental disorders, and whichshould thus
be also considered as prime candidate sub-strates of functional
significance. Moreover, 4 of the 168CDK6 interactors listed in the
Biogrid database are
involved in human disorders that include microcephaly.Although
this could result from a purely random coinci-dence, these
candidate interactors, which were mostlyidentified by
high-throughput approaches, should beconsidered with higher
scrutiny. MPPH syndromes canbe caused by activating mutations in
the genes codingfor AKT3 or for the regulatory or catalytic subunit
ofPI3K [81]. Activation of the PI3K-AKT pathway isknown to inhibit
GSK-3β, a protein kinase that phos-phorylates and tags cyclin D2
for degradation [44]. Ascould be expected, cyclin D2 is stabilized
in cells derivedfrom MPPH patients with activating mutations on
thePI3K-AKT axis. This strongly points cyclin D2stabilization as
the shared endpoint of the MPPH syn-dromes (Fig. 2).
Fig. 1 CDK5-centered regulatory network and its involvement in
human neurodevelopmental disorders. PAFAH1B1 (aka LIS1) and YWHAE
bind toCDK5/p35-phosphorylated NUDEL, thereby protecting it from
degradation. Two other proteins involved in lissencephalic
syndromes, DCX andNDE1 (aka LISX1 and LIS4, respectively), are also
phosphorylated and regulated by CDK5, which thus plays a central
role in the neuronaldevelopment mechanisms underlying
lissencephaly
Fig. 2 CDK6/CycD2-centered regulatory network and its
involvement in human neurodevelopmental disorders. Cyclin D2
stabilization causesMPPH and can be caused by mutations in the
CCND2 gene or in the genes coding for AKT or for the PI3K subunits,
which result in GSK3βphosphorylation and inhibition. A number of
CDK6 putative phosphorylation substrates and putative interacting
partners are involved in MCPH,other microcephalic syndromes, or
other neurodevelopmental syndromes. Data sources: the Online
Mendelian Inheritance in Man database(www.omim.org) and the
Biological General Repository for Interaction Datasets
(www.thebiogrid.org)
Colas Orphanet Journal of Rare Diseases (2020) 15:203 Page 9 of
14
http://www.omim.orghttp://www.thebiogrid.org
-
STAR syndrome presents a strong clinical overlap
withTownes-Brocks syndrome (TBS), so much so that someSTAR patients
have been initially diagnosed with TBS[32]. Because TBS is caused
by mutations on the tran-scriptional repressor SALL1 [82], it was
hypothesizedand demonstrated that cyclin M and SALL1 interact,akin
to their respective paralogs cyclin D1 and SALL4[29]. The function
of this interaction remains to bedetermined.Cyclin K was recently
found to interact with the his-
tone methyltransferase SETD1A that recruits it to
thechromosomes, where it is required to ensure DNA dam-age response
by controlling the expression of genes in-volved in DNA repair
[83]. Interestingly, loss-of-functionmutations in SETD1A are
associated to schizophreniaand intellectual disabilities [84], the
latter being observedin all CCNK-deficient patients. A number of
high-throughput studies have identified putative CDK13 and/or
cyclin K interacting partners, some of which are in-volved in human
disorders that present overlapping phe-notypes with the syndromes
caused by loss-of-functionmutations in CDK13 and CCNK genes. For
example,ACTC1 is involved in a number of heart defects, amongwhich
is atrial septal defect, frequently observed inCDK13-deficient
patients [53]. Here again, these putativeinteractions should be
further explored with more atten-tion than others (Fig. 3).
Edgotyping CDK and cyclin pathogenic variantsMissense mutations
represent more than half of re-ported mutations that cause
Mendelian disorders [85].The previously mentioned large-scale
analysis of DNMscausing developmental disorders revealed that 23%
ofthe individuals carry missense or protein-truncating mu-tations
[13]. Nonsense or frameshift mutations introducepremature
termination codons, which, depending ontheir localization in the
genes, can be insensitive toNMD and allow the expression of
truncated proteins
(reviewed in [86]). Missense or protein-truncating muta-tions
can either compromise the structure of proteins,which are then
usually degraded by the proteasome, orcompromise specific
interactions with other (macro)-molecules. A large-scale study on
almost 3000 missensemutations concerning 1140 genes revealed that a
major-ity of disease-causing mutations do not dramaticallyaffect
protein structure or folding. Interestingly, whilecommon variants
rarely affect interactions, two-thirds ofpathogenic variants show
perturbed protein interactionprofiles, half of which presenting
selective losses of inter-actions [87]. Edgotyping (i.e.
determining the interactionprofiles of) such “edgetic” variants can
be extremely in-formative on pathogenic mechanisms and on the
func-tions exerted by crucially important protein
interactions.Among the plethora of protein interaction assays
thathave been developed, transcriptional yeast two-hybridmating
assays are particularly well suited for this pur-pose [88].A number
of CDK /cyclin mutations reviewed herein
likely produce edgetic variants, which remain to be
char-acterized. CDK13 pathogenic missense mutations in thekinase
domain are thought to compromise CDK13 cata-lytic activity by
causing loss of ATP binding whileretaining its capacity to interact
with cyclin K, therebyacting as dominant negative mutants [16].
However, anumber of patients present protein-truncating
mutationsthat occur in the 5′ half of the gene, which rather
pointsto haploinsufficiency. Edgotyping the diverse set
ofpathogenic CDK13 variants should illuminate the mo-lecular
etiology of the syndrome. Likewise, such an effortwould directly
test the hypothesized loss of interactionbetween the cyclin K K111E
pathogenic variant andCDK13 (and CDK12) [23]. Edgotyping the CDK6
A197Tpathogenic variant should confirm its ability to retainthe
interactions with cyclin D and the INK inhibitor [8],and it might
provide an explanation for the fact that itno longer localizes in
centrosomes if a loss of interaction
Fig. 3 CDK13/CycK-centered regulatory network and its
involvement in human developmental and behavioral disorders. Except
for the CDK13-CycK and CycK-SETD1A interactions, all other
interactions have been detected by high-throughput studies and are
thus putative. EZH2 and DVL3are involved in the Weaver and Robinow
syndromes, respectively. Data sources: same as Fig. 2
Colas Orphanet Journal of Rare Diseases (2020) 15:203 Page 10 of
14
-
with a known centrosomal protein is detected (Fig. 4).The
inability to detect expression of cyclin O pathogenicvariants (and
in particular that of a 321 AA truncatedvariant) [24] is unlikely
due to mRNA NMD and mightresult from a compromised interaction that
normallystabilizes the wild-type protein. Edgotyping these
trun-cated cyclin O forms and the two reported missense var-iants
(one of which being detectably expressed [26])should prove very
informative.
ConclusionOver the past decade, the harnessing of
next-generationsequencing methods to understand human genetic
dis-eases has considerably accelerated the discovery ofpathological
mutations. So far, mutations in 6 CDKs and4 cyclins have been
involved in rare human developmen-tal disorders. Considering the
importance and the varietyof functions exerted by CDKs and cyclins
in cellular pro-cesses that play crucial roles in development,
mutationsin additional members of both families will undoubtedlybe
discovered in other syndromes. As highlighted herein,some of these
future discoveries will probably revealnew functions even for those
CDKs and cyclins that havebeen thoroughly studied for the past 30
years. Crossing
various data obtained from genome and proteome-scaleendeavors,
such as protein interaction databases, withexisting and future
human genetics knowledge will allowto further chart regulatory
networks around CDK / cyc-lin complexes and other important
regulators. These ex-panded regulatory networks will be fruitfully
exploitedto edgotype missense and truncated CDK / cyclin
patho-genic variants, which will strengthen our knowledge onthese
proteins and illuminate pathogenic mechanisms.Finally, although
most CDK / cyclin-related disordersstem from abnormal development,
few of them (and es-pecially those caused by gain-of-function
mutations)might conceivably offer opportunities of therapeutic
in-terventions to alleviate some symptoms, using increas-ingly
selective CDK inhibitors that are currently and willbe developed as
drugs [89].
AbbreviationsATP: Adenosine triphosphate; BBS: Bardet-Biedl
syndrome; CDK: Cyclin-dependent kinase; CTD: C-terminal domain;
DNM: De novo mutations;gnomAD: Genome aggregation database; KO:
Knockout; LCH: Lissencephalywith cerebellar hypoplasia; MCPH:
Autosomal recessive primarymicrocephaly; MMC: Multiple motile
cilia; MPPH:
Megalencephaly-polymicrogyria-polydactyly-hydrocephaly; NMD:
Non-sense mediated decay;NS-ID: Non-syndromic intellectual
disability; PCD: Primary ciliary dyskinesia;
Fig. 4 Edgotyping disease-causing protein variants. a left: a
wild-type protein (red) interacts with 5 different proteins;
middle: all interactions arelost because the protein is no longer
expressed (gene deletion, nonsense or frameshift mutations causing
mRNA NMD), or its structure is severelycompromised (all kinds of
mutations); right: only one of the interactions is lost
(truncation-inducing or missense mutation). b Edgotyping of theCDK6
A197T variant, which is suspected to retain its enzymatic activity
but which no longer localizes in the centrosomes because of a
hypotheticloss of interaction with a centrosomal protein that
remains to be identified
Colas Orphanet Journal of Rare Diseases (2020) 15:203 Page 11 of
14
-
RNAi: RNA interference; RNA pol II: RNA polymerase II; STAR:
Syndactilytelecanthus anorectal; TBS: Townes-Brocks syndrome
AcknowledgementsI am grateful to Anne-Catherine Dock-Bregeon for
her critical reading of themanuscript. I apologize for the
omissions of relevant work and references.
Author’s contributionsThe author(s) read and approved the final
manuscript.
FundingI thank the Ligue Nationale contre le Cancer Grand Ouest
for supporting ourwork on CDK10/CycM.
Availability of data and materialsNot applicable.
Ethics approval and consent to participateNot applicable.
Consent for publicationNot applicable.
Competing interestsThe author declares that he has no competing
interests.
Received: 22 April 2020 Accepted: 21 July 2020
References1. Malumbres M. Cyclin-dependent kinases. Genome Biol.
2014;15(6):122.2. Hydbring P, Malumbres M, Sicinski P.
Non-canonical functions of cell cycle
cyclins and cyclin-dependent kinases. Nat Rev Mol Cell Biol.
2016;17(5):280–92.3. Quandt E, Ribeiro MPC, Clotet J. Atypical
cyclins: the extended family
portrait. Cell Mol Life Sci. 2020;77(2):231–42.4. Schettini F,
De Santo I, Rea CG, De Placido P, Formisano L, Giuliano M, et
al.
CDK 4/6 Inhibitors as Single Agent in Advanced Solid Tumors.
Frontiers inoncology. 2018;8:608.
5. Toussi A, Mans N, Welborn J, Kiuru M. Germline mutations
predisposing tomelanoma. J Cutaneous Pathol. 2020;47(7):606-16.
6. Petersen BS, Fredrich B, Hoeppner MP, Ellinghaus D, Franke A.
Opportunitiesand challenges of whole-genome and -exome sequencing.
BMC Genet.2017;18(1):14.
7. Magen D, Ofir A, Berger L, Goldsher D, Eran A, Katib N, et
al. Autosomalrecessive lissencephaly with cerebellar hypoplasia is
associated with a loss-of-function mutation in CDK5. Hum Genet.
2015;134(3):305–14.
8. Hussain MS, Baig SM, Neumann S, Peche VS, Szczepanski S,
Nurnberg G,et al. CDK6 associates with the centrosome during
mitosis and is mutatedin a large Pakistani family with primary
microcephaly. Hum Mol Genet. 2013;22(25):5199–214.
9. Calpena E, Hervieu A, Kaserer T, Swagemakers SMA, Goos JAC,
Popoola O,et al. De Novo Missense Substitutions in the Gene
Encoding CDK8, aRegulator of the Mediator Complex, Cause a
Syndromic DevelopmentalDisorder. Am J Hum Genet.
2019;104(4):709–20.
10. Windpassinger C, Piard J, Bonnard C, Alfadhel M, Lim S,
Bisteau X, et al.CDK10 Mutations in Humans and Mice Cause Severe
Growth Retardation,Spine Malformations, and Developmental Delays.
Am J Hum Genet. 2017;101(3):391–403.
11. Guen VJ, Edvardson S, Fraenkel ND, Fattal-Valevski A, Jalas
C, Anteby I, et al.A homozygous deleterious CDK10 mutation in a
patient with agenesis ofcorpus callosum, retinopathy, and deafness.
Am J Med Genet A. 2018;176(1):92–8.
12. Sifrim A, Hitz MP, Wilsdon A, Breckpot J, Turki SH,
Thienpont B, et al. Distinctgenetic architectures for syndromic and
nonsyndromic congenital heartdefects identified by exome
sequencing. Nat Genet. 2016;48(9):1060–5.
13. Deciphering Developmental Disorders S. Prevalence and
architecture of denovo mutations in developmental disorders.
Nature. 2017;542(7642):433–8.
14. Bostwick BL, McLean S, Posey JE, Streff HE, Gripp KW,
Blesson A, et al.Phenotypic and molecular characterisation of
CDK13-related congenitalheart defects, dysmorphic facial features
and intellectual developmentaldisorders. Genome Med.
2017;9(1):73.
15. Carneiro TN, Krepischi AC, Costa SS, Tojal da Silva I,
Vianna-Morgante AM,Valieris R, et al. Utility of trio-based exome
sequencing in the elucidation ofthe genetic basis of isolated
syndromic intellectual disability: illustrativecases. Appl Clin
Genet. 2018;11:93–8.
16. Hamilton MJ, Caswell RC, Canham N, Cole T, Firth HV, Foulds
N, et al.Heterozygous mutations affecting the protein kinase domain
of CDK13cause a syndromic form of developmental delay and
intellectual disability. JMed Genet. 2018;55(1):28–38.
17. Uehara T, Takenouchi T, Kosaki R, Kurosawa K, Mizuno S,
Kosaki K.Redefining the phenotypic spectrum of de novo heterozygous
CDK13variants: Three patients without cardiac defects. Eur J Med
Genet. 2018;61(5):243–7.
18. van den Akker WMR, Brummelman I, Martis LM, Timmermans RN,
Pfundt R,Kleefstra T, et al. De novo variants in CDK13 associated
with syndromic ID/DD: Molecular and clinical delineation of 15
individuals and a furtherreview. Clin Genet. 2018;93(5):1000–7.
19. Yakubov R, Ayman A, Kremer AK, van den Akker M.
One-month-old girlpresenting with pseudohypoaldosteronism leading
to the diagnosis ofCDK13-related disorder: a case report and review
of the literature. J MedCase Rep. 2019;13(1):386.
20. Trinh J, Kandaswamy KK, Werber M, Weiss MER, Oprea G,
Kishore S, et al.Novel pathogenic variants and multiple molecular
diagnoses inneurodevelopmental disorders. J Neurodev Disord.
2019;11(1):11.
21. Mukhopadhyay A, Kramer JM, Merkx G, Lugtenberg D, Smeets DF,
OortveldMA, et al. CDK19 is disrupted in a female patient with
bilateral congenitalretinal folds, microcephaly and mild mental
retardation. Hum Genet. 2010;128(3):281–91.
22. Mirzaa G, Parry DA, Fry AE, Giamanco KA, Schwartzentruber J,
Vanstone M,et al. De novo CCND2 mutations leading to stabilization
of cyclin D2
causemegalencephaly-polymicrogyria-polydactyly-hydrocephalus
syndrome. NatGenet. 2014;46(5):510–5.
23. Fan Y, Yin W, Hu B, Kline AD, Zhang VW, Liang D, et al. De
Novo Mutationsof CCNK Cause a Syndromic Neurodevelopmental Disorder
with DistinctiveFacial Dysmorphism. Am J Hum Genet.
2018;103(3):448–55.
24. Wallmeier J, Al-Mutairi DA, Chen CT, Loges NT, Pennekamp P,
Menchen T,et al. Mutations in CCNO result in congenital mucociliary
clearancedisorder with reduced generation of multiple motile cilia.
Nat Genet.2014;46(6):646–51.
25. Casey JP, McGettigan PA, Healy F, Hogg C, Reynolds A,
Kennedy BN, et al.Unexpected genetic heterogeneity for primary
ciliary dyskinesia in the IrishTraveller population. Eur J Hum
Genet. 2015;23(2):210–7.
26. Amirav I, Wallmeier J, Loges NT, Menchen T, Pennekamp P,
Mussaffi H, et al.Systematic Analysis of CCNO Variants in a Defined
Population: Implicationsfor Clinical Phenotype and Differential
Diagnosis. Hum Mutat. 2016;37(4):396–405.
27. Guo T, Tan ZP, Chen HM, Zheng DY, Liu L, Huang XG, et al. An
effectivecombination of whole-exome sequencing and runs of
homozygosity forthe diagnosis of primary ciliary dyskinesia in
consanguineous families. SciRep. 2017;7(1):7905.
28. Emiralioglu N, Taskiran EZ, Kosukcu C, Bilgic E, Atilla P,
Kaya B, et al.Genotype and phenotype evaluation of patients with
primary ciliarydyskinesia: First results from Turkey. Pediatr
Pulmonol. 2020;55(2):383–93.
29. Unger S, Bohm D, Kaiser FJ, Kaulfuss S, Borozdin W, Buiting
K, et al.Mutations in the cyclin family member FAM58A cause an
X-linkeddominant disorder characterized by syndactyly, telecanthus
and anogenitaland renal malformations. Nat Genet.
2008;40(3):287–9.
30. Boone PM, Bacino CA, Shaw CA, Eng PA, Hixson PM, Pursley AN,
et al.Detection of clinically relevant exonic copy-number changes
by array CGH.Hum Mutat. 2010;31(12):1326–42.
31. Zarate YA, Farrell JM, Alfaro MP, Elhassan NO. STAR syndrome
is part of thedifferential diagnosis of females with anorectal
malformations. Am J MedGenet A. 2015;167A(8):1940–3.
32. Orge FH, Dar SA, Blackburn CN, Grimes-Hodges SJ, Mitchell
AL. Ocularmanifestations of X-linked dominant FAM58A mutation in
toe syndactyly,telecanthus, anogenital, and renal malformations
('STAR') syndrome.Ophthalmic Genet. 2016;37(3):323–7.
33. Boczek NJ, Kruisselbrink T, Cousin MA, Blackburn PR, Klee
EW, Gavrilova RH, et al.Multigenerational pedigree with STAR
syndrome: A novel FAM58A variant andexpansion of the phenotype. Am
J Med Genet A. 2017;173(5):1328–33.
34. Lefroy H, Hurst JA, Shears DJ. STAR syndrome: a further case
and the firstreport of maternal mosaicism. Clin Dysmorphol.
2017;26(3):157–60.
Colas Orphanet Journal of Rare Diseases (2020) 15:203 Page 12 of
14
-
35. Bedeschi MF, Giangiobbe S, Paganini L, Tabano S, Silipigni
R, Colombo L,et al. STAR syndrome plus: The first description of a
female patient with thelethal form. Am J Med Genet A.
2017;173(12):3226–30.
36. Tan AP, Chong WK, Mankad K. Comprehensive
genotype-phenotypecorrelation in lissencephaly. Quant Imag Med
Surg. 2018;8(7):673–93.
37. Tarricone C, Dhavan R, Peng J, Areces LB, Tsai LH, Musacchio
A. Structureand regulation of the CDK5-p25(nck5a) complex. Mol
Cell. 2001;8(3):657–69.
38. Shah K, Lahiri DK. Cdk5 activity in the brain - multiple
paths of regulation. JCell Sci. 2014;127(Pt 11):2391–400.
39. Moncini S, Castronovo P, Murgia A, Russo S, Bedeschi MF,
Lunghi M, et al.Functional characterization of CDK5 and CDK5R1
mutations identified inpatients with non-syndromic intellectual
disability. J Hum Genet. 2016;61(4):283–93.
40. Zhou X, Zhi Y, Yu J, Xu D. The Yin and Yang of Autosomal
RecessivePrimary Microcephaly Genes: Insights from Neurogenesis
andCarcinogenesis. Int J Mol Sci. 2020;21(5).
41. Tigan AS, Bellutti F, Kollmann K, Tebb G, Sexl V. CDK6-a
review of the pastand a glimpse into the future: from cell-cycle
control to transcriptionalregulation. Oncogene.
2016;35(24):3083–91.
42. Cappuccio G, Ugga L, Parrini E, D'Amico A, Brunetti-Pierri
N. Severepresentation and complex brain malformations in an
individual carrying aCCND2 variant. Mol Genet Genom Med.
2019;7(6):e708.
43. Sameshima T, Morisada N, Egawa T, Kugo M, Iijima K. MPPH
syndrome withaortic coarctation and macrosomia due to CCND2
mutations. Pediatr Int.2020;62(1):115–7.
44. Kida A, Kakihana K, Kotani S, Kurosu T, Miura O. Glycogen
synthase kinase-3beta and p38 phosphorylate cyclin D2 on Thr280 to
trigger its ubiquitin/proteasome-dependent degradation in
hematopoietic cells. Oncogene.2007;26(46):6630–40.
45. Glickstein SB, Alexander S, Ross ME. Differences in cyclin
D2 and D1 proteinexpression distinguish forebrain progenitor
subsets. Cerebral Cortex. 2007;17(3):632–42.
46. Green AJ, Sandford RN, Davison BC. An autosomal dominant
syndrome ofrenal and anogenital malformations with syndactyly. J
Med Genet. 1996;33(7):594–6.
47. Guen VJ, Gamble C, Flajolet M, Unger S, Thollet A, Ferandin
Y, et al. CDK10/cyclin M is a protein kinase that controls ETS2
degradation and is deficientin STAR syndrome. Proc Natl Acad Sci U
S A. 2013;110(48):19525–30.
48. Sumarsono SH, Wilson TJ, Tymms MJ, Venter DJ, Corrick CM,
Kola R, et al.Down's syndrome-like skeletal abnormalities in Ets2
transgenic mice. Nature.1996;379(6565):534–7.
49. Guen VJ, Gamble C, Perez DE, Bourassa S, Zappel H, Gartner
J, et al. STARsyndrome-associated CDK10/Cyclin M regulates actin
network architectureand ciliogenesis. Cell Cycle.
2016;15(5):678–88.
50. Sergere JC, Thuret JY, Le Roux G, Carosella ED, Leteurtre F.
Human CDK10gene isoforms. Biochem Biophys Res Commun.
2000;276(1):271–7.
51. Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E,
Fennell T, et al.Analysis of protein-coding genetic variation in
60,706 humans. Nature. 2016;536(7616):285–91.
52. Zimmermann M, Arachchige-Don AP, Donaldson MS, Patriarchi T,
HorneMC. Cyclin G2 promotes cell cycle arrest in breast cancer
cells respondingto fulvestrant and metformin and correlates with
patient survival. Cell Cycle.2016;15(23):3278–95.
53. Hamilton MJ, Suri M. CDK13-related disorder. Adv Genet.
2019;103:163–82.54. Even Y, Durieux S, Escande ML, Lozano JC,
Peaucellier G, Weil D, et al. CDC2L5,
a Cdk-like kinase with RS domain, interacts with the
ASF/SF2-associatedprotein p32 and affects splicing in vivo. J Cell
Biochem. 2006;99(3):890–904.
55. Blazek D, Kohoutek J, Bartholomeeusen K, Johansen E,
Hulinkova P, Luo Z, et al.The Cyclin K/Cdk12 complex maintains
genomic stability via regulation ofexpression of DNA damage
response genes. Genes Dev. 2011;25(20):2158–72.
56. Greifenberg AK, Honig D, Pilarova K, Duster R,
Bartholomeeusen K, BoskenCA, et al. Structural and Functional
Analysis of the Cdk13/Cyclin K Complex.Cell Rep.
2016;14(2):320–31.
57. van den Heuvel S, Harlow E. Distinct roles for
cyclin-dependent kinases incell cycle control. Science.
1993;262(5142):2050–4.
58. Bosken CA, Farnung L, Hintermair C, Merzel Schachter M,
Vogel-Bachmayr K,Blazek D, et al. The structure and substrate
specificity of human Cdk12/Cyclin K. Nat Commun. 2014;5:3505.
59. Dai Q, Lei T, Zhao C, Zhong J, Tang YZ, Chen B, et al.
Cyclin K-containingkinase complexes maintain self-renewal in murine
embryonic stem cells. JBiol Chem. 2012;287(30):25344–52.
60. Chen HR, Lin GT, Huang CK, Fann MJ. Cdk12 and Cdk13 regulate
axonalelongation through a common signaling pathway that modulates
Cdk5expression. Exp Neurol. 2014;261:10–21.
61. Fu TJ, Peng J, Lee G, Price DH, Flores O. Cyclin K functions
as a CDK9regulatory subunit and participates in RNA polymerase II
transcription. J BiolChem. 1999;274(49):34527–30.
62. Spassky N, Meunier A. The development and functions of
multiciliatedepithelia. Nat Rev Mol Cell Biol.
2017;18(7):423–36.
63. Soutourina J. Transcription regulation by the Mediator
complex. Nat RevMol Cell Biol. 2018;19(4):262–74.
64. Dannappel MV, Sooraj D, Loh JJ, Firestein R. Molecular and
in vivo Functionsof the CDK8 and CDK19 Kinase Modules. Front Cell
Dev Biol. 2018;6:171.
65. Glickstein SB, Monaghan JA, Koeller HB, Jones TK, Ross ME.
Cyclin D2 iscritical for intermediate progenitor cell proliferation
in the embryoniccortex. J Neurosci. 2009;29(30):9614–24.
66. Kim J, Lee JE, Heynen-Genel S, Suyama E, Ono K, Lee K, et
al. Functionalgenomic screen for modulators of ciliogenesis and
cilium length. Nature.2010;464(7291):1048–51.
67. Funk MC, Bera AN, Menchen T, Kuales G, Thriene K, Lienkamp
SS, et al.Cyclin O (Ccno) functions during deuterosome-mediated
centrioleamplification of multiciliated cells. EMBO J.
2015;34(8):1078–89.
68. Nunez-Olle M, Jung C, Terre B, Balsiger NA, Plata C, Roset
R, et al.Constitutive Cyclin O deficiency results in penetrant
hydrocephalus,impaired growth and infertility. Oncotarget.
2017;8(59):99261–73.
69. Maddirevula S, Awartani K, Coskun S, AlNaim LF, Ibrahim N,
Abdulwahab F,et al. A genomics approach to females with infertility
and recurrentpregnancy loss. Hum Genet. 2020.
70. Westerling T, Kuuluvainen E, Makela TP. Cdk8 is essential
for preimplantationmouse development. Mol Cell Biol.
2007;27(17):6177–82.
71. Satyanarayana A, Kaldis P. Mammalian cell-cycle regulation:
several Cdks,numerous cyclins and diverse compensatory mechanisms.
Oncogene. 2009;28(33):2925–39.
72. Brown SDM, Holmes CC, Mallon AM, Meehan TF, Smedley D, Wells
S. High-throughput mouse phenomics for characterizing mammalian
genefunction. Nat Rev Genet. 2018;19(6):357–70.
73. Birling MC, Herault Y, Pavlovic G. Modeling human disease in
rodents byCRISPR/Cas9 genome editing. Mammalian genome.
2017;28(7-8):291–301.
74. Suspitsin EN, Imyanitov EN. Bardet-Biedl Syndrome. Mol
Syndromol. 2016;7(2):62–71.
75. Caro-Llopis A, Rosello M, Orellana C, Oltra S, Monfort S,
Mayo S, et al. Denovo mutations in genes of mediator complex
causing syndromicintellectual disability: mediatorpathy or
transcriptomopathy? Pediatr Res.2016;80(6):809–15.
76. Shah K, Lahiri DK. A Tale of the Good and Bad: Remodeling of
the MicrotubuleNetwork in the Brain by Cdk5. Mol Neurobiol.
2017;54(3):2255–68.
77. Kodani A, Kenny C, Lai A, Gonzalez DM, Stronge E, Sejourne
GM, et al.Posterior Neocortex-Specific Regulation of Neuronal
Migration by CEP85LIdentifies Maternal Centriole-Dependent
Activation of CDK5. Neuron. 2020;106(2):246-55.
78. Anders L, Ke N, Hydbring P, Choi YJ, Widlund HR, Chick JM,
et al. Asystematic screen for CDK4/6 substrates links FOXM1
phosphorylation tosenescence suppression in cancer cells. Cancer
Cell. 2011;20(5):620–34.
79. Dias C, Estruch SB, Graham SA, McRae J, Sawiak SJ, Hurst JA,
et al. BCL11AHaploinsufficiency Causes an Intellectual Disability
Syndrome andDysregulates Transcription. Am J Hum Genet.
2016;99(2):253–74.
80. Luc S, Huang J, McEldoon JL, Somuncular E, Li D, Rhodes C,
et al. Bcl11aDeficiency Leads to Hematopoietic Stem Cell Defects
with an Aging-likePhenotype. Cell Rep. 2016;16(12):3181–94.
81. Riviere JB, Mirzaa GM, O'Roak BJ, Beddaoui M, Alcantara D,
Conway RL, et al.De novo germline and postzygotic mutations in
AKT3, PIK3R2 and PIK3CAcause a spectrum of related megalencephaly
syndromes. Nat Genet. 2012;44(8):934–40.
82. Kohlhase J, Wischermann A, Reichenbach H, Froster U, Engel
W. Mutationsin the SALL1 putative transcription factor gene cause
Townes-Brockssyndrome. Nat Genet. 1998;18(1):81–3.
83. Hoshii T, Cifani P, Feng Z, Huang CH, Koche R, Chen CW, et
al. A Non-catalytic Function of SETD1A Regulates Cyclin K and the
DNA DamageResponse. Cell. 2018;172(5):1007–21 e17.
84. Singh T, Kurki MI, Curtis D, Purcell SM, Crooks L, McRae J,
et al. Rare loss-of-function variants in SETD1A are associated with
schizophrenia anddevelopmental disorders. Nat Neurosci.
2016;19(4):571–7.
Colas Orphanet Journal of Rare Diseases (2020) 15:203 Page 13 of
14
-
85. Stenson PD, Mort M, Ball EV, Shaw K, Phillips A, Cooper DN.
The HumanGene Mutation Database: building a comprehensive mutation
repository forclinical and molecular genetics, diagnostic testing
and personalizedgenomic medicine. Hum Genet. 2014;133(1):1–9.
86. Kurosaki T, Popp MW, Maquat LE. Quality and quantity control
of geneexpression by nonsense-mediated mRNA decay. Nat Rev Mol Cell
Biol. 2019;20(7):406–20.
87. Sahni N, Yi S, Taipale M, Fuxman Bass JI,
Coulombe-Huntington J, Yang F,et al. Widespread macromolecular
interaction perturbations in humangenetic disorders. Cell.
2015;161(3):647–60.
88. Hamdi A, Colas P. Yeast two-hybrid methods and their
applications in drugdiscovery. Trends Pharmacol Sci.
2012;33(2):109–18.
89. Roskoski R Jr. Cyclin-dependent protein serine/threonine
kinase inhibitors asanticancer drugs. Pharmacol Res.
2019;139:471–88.
Publisher’s NoteSpringer Nature remains neutral with regard to
jurisdictional claims inpublished maps and institutional
affiliations.
Colas Orphanet Journal of Rare Diseases (2020) 15:203 Page 14 of
14
AbstractIntroductionCDK5 and lissencephaly with cerebellar
hypoplasiaCDK6 and primary microcephalyCyclin D2 and
megalencephaly-polymicrogyria-polydactyly-hydrocephalus
syndromeCyclin M and STAR syndromeCDK10 and Al Kaissi syndromeCDK13
and a congenital heart defect, craniofacial and intellectual
development syndromeCyclin K and a neurodevelopmental
disorder/facial dysmorphism syndromeCyclin O and congenital
mucociliary clearance disorderCDK19 / CDK8 and syndromic
developmental disorders with intellectual disabilityHuman
developmental syndromes reveal CDK/cyclin functionsCDK/cyclin human
disorders are variably phenocopied by mouse modelsHuman genetics
looms CDK/cyclin regulatory networksEdgotyping CDK and cyclin
pathogenic variants
ConclusionAbbreviationsAcknowledgementsAuthor’s
contributionsFundingAvailability of data and materialsEthics
approval and consent to participateConsent for publicationCompeting
interestsReferencesPublisher’s Note